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app.R
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# # BGC3D
# A shiny app for visualizing biogeoclimatic units in 3D climate space
# Colin Mahony colin.mahony@gov.bc.ca
# Copyright 2021 Province of British Columbia
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
library(shiny)
library(rgl)
library(sf)
library(leaflet)
library(leafem)
library(htmlwidgets)
library(leaflet.opacity)
library(raster)
# ------------------------------------------
# Load the input data
# ------------------------------------------
#BGC zone color scheme
BGCcolors.BC <- read.csv("data/BGCzone_Colorscheme.csv")
BGCcolors <- read.csv("data/WNAv11_Zone_Colours.csv")
BGCcolors$colour <- as.character(BGCcolors$colour)
BGCcolors$colour[match(BGCcolors.BC$zone, BGCcolors$classification)] <- as.character(BGCcolors.BC$HEX)
ColScheme.zone <- factor(BGCcolors$colour, levels=BGCcolors$colour)
zones <- factor(BGCcolors$classification, levels=BGCcolors$classification)
# BGC labels
BGCs.BC <- read.csv("data/Clim.BGCs.BC.csv")[,1]
BGCs.WNA <- read.csv("data/Clim.BGCs.WNA.csv")[,1]
BGCs.sample.BC <- read.csv("data/Clim.sample.BC.csv")[,1]
BGCs.sample.WNA <- read.csv("data/Clim.sample.WNA.csv")[,1]
BGCs.future <- read.csv("data/Clim.BGCs.BC.future.csv")[,1]
scenario <- read.csv("data/Clim.BGCs.BC.future.csv")[,2:4]
rcps <- sort(unique(scenario[,2]))
proj.years <- unique(scenario[,3])
# Geographic Data
Geog.BGCs.BC <- read.csv("data/Clim.BGCs.BC.csv")[,c(3,2,4)]
Geog.BGCs.WNA <- read.csv("data/Clim.BGCs.WNA.csv")[,c(3,2,4)]
Geog.BGCs.BC.2004 <- read.csv("data/Clim.BGCs.BC.2004.csv")[,c(3,2,4)]
Geog.sample.BC <- read.csv("data/Clim.sample.BC.csv")[,c(3,2,4)]
Geog.sample.WNA <- read.csv("data/Clim.sample.WNA.csv")[,c(3,2,4)]
Geog.BGCs.BC.future <- read.csv("data/Clim.BGCs.BC.future.csv")[,c(6,5,7)]
# Climate Data
Clim.BGCs.BC.all <- read.csv("data/Clim.BGCs.BC.csv")[,-c(1:4)]
Clim.BGCs.WNA.all <- read.csv("data/Clim.BGCs.WNA.csv")[,-c(1:4)]
Clim.BGCs.BC.2004.all <- read.csv("data/Clim.BGCs.BC.2004.csv")[,-c(1:4)]
Clim.sample.BC.all <- read.csv("data/Clim.sample.BC.csv")[,-c(1:4)]
Clim.sample.WNA.all <- read.csv("data/Clim.sample.WNA.csv")[,-c(1:4)]
Clim.BGCs.BC.future.all <- read.csv("data/Clim.BGCs.BC.future.csv")[,-c(1:6)]
Clim.BGCs.BC.future.all <- Clim.BGCs.BC.future.all[which(names(Clim.BGCs.BC.future.all)%in%names(Clim.BGCs.BC.all))]
# # reorder variables
# Clim.BGCs.BC.all <- Clim.BGCs.BC.all [,order(names(Clim.BGCs.BC.all ))]
# Clim.BGCs.WNA.all <- Clim.BGCs.WNA.all [,order(names(Clim.BGCs.WNA.all ))]
# Clim.BGCs.BC.2004.all <- Clim.BGCs.BC.2004.all [,order(names(Clim.BGCs.BC.2004.all ))]
# Clim.sample.BC.all <- Clim.sample.BC.all [,order(names(Clim.sample.BC.all ))]
# Clim.sample.WNA.all <- Clim.sample.WNA.all [,order(names(Clim.sample.WNA.all ))]
# Clim.BGCs.BC.future.all <- Clim.BGCs.BC.future.all [,order(names(Clim.BGCs.BC.future.all ))]
# # remove CMD (too skewed for PCA)
# Clim.BGCs.BC <- Clim.BGCs.BC[-grep("CMD", names(Clim.BGCs.BC))]
# Clim.BGCs.WNA <- Clim.BGCs.WNA[-grep("CMD", names(Clim.BGCs.WNA))]
# Clim.BGCs.BC.2004 <- Clim.BGCs.BC.2004[-grep("CMD", names(Clim.BGCs.BC.2004))]
# Clim.sample.BC <- Clim.sample.BC[-grep("CMD", names(Clim.sample.BC))]
# Clim.sample.WNA <- Clim.sample.WNA[-grep("CMD", names(Clim.sample.WNA))]
# Clim.BGCs.BC.future <- Clim.BGCs.BC.future[-grep("CMD", names(Clim.BGCs.BC.future))]
#
# # PC Scores without log transformation
# pca.BGCs <- prcomp(Clim.BGCs.BC, scale=T)
# # Cor <- cor(Clim.BGCs.BC,predict(pca.BGCs, logT.clim(Clim.BGCs.BC)))
# Clim.BGCs.BC <- cbind(predict(pca.BGCs, Clim.BGCs.BC)[,1:3], Clim.BGCs.BC)
# Clim.BGCs.WNA <- cbind(predict(pca.BGCs, Clim.BGCs.WNA)[,1:3],Clim.BGCs.WNA)
# Clim.BGCs.BC.2004 <- cbind(predict(pca.BGCs, Clim.BGCs.BC.2004)[,1:3],Clim.BGCs.BC.2004)
# Clim.sample.BC <- cbind(predict(pca.BGCs, Clim.sample.BC)[,1:3],Clim.sample.BC)
# Clim.sample.WNA <- cbind(predict(pca.BGCs, Clim.sample.WNA)[,1:3],Clim.sample.WNA)
# Clim.BGCs.BC.future <- cbind(predict(pca.BGCs, Clim.BGCs.BC.future)[,1:3],Clim.BGCs.BC.future)
zones.BC <- rep(NA, length(BGCs.BC))
for(i in BGCcolors$classification){ zones.BC[grep(i,BGCs.BC)] <- i }
zones.BC <- factor(zones.BC, BGCcolors$classification)
zones.WNA <- rep(NA, length(BGCs.WNA))
for(i in BGCcolors$classification){ zones.WNA[grep(i,BGCs.WNA)] <- i }
zones.WNA <- factor(zones.WNA, BGCcolors$classification)
vars.cbst <- c("Latitude", "MAT", "MCMT", "TD", "MAP", "MSP", "DD5", "PAS")
vars.basic <- paste(rep(c("Tmin", "Tmax", "PPT"), each=4), rep(c("wt", "sp", "sm", "at"), times=4), sep="_")
vars.cciss <- c("CMD.total", "DD5_sp", "PPT_JAS", "bFFP", "MCMT", "AHM", "CMD_sp", "CMDMax", "DD5", "DD5_sm", "Eref_sm", "Eref_sp", "MWMT", "NFFD", "PAS_sp", "PAS_wt", "PPT_MJ", "SHM", "Tmax_sm")
varsets <- c("basic", "cbst", "cciss")
variable.names <- read.csv("data/Variables_ClimateBC.csv")
## SPATIAL DATA
bgc.simple <- st_read("data/bgc.simple.shp")
bgc.maprecord <- as.character(bgc.simple$BGC)
zone.maprecord <- bgc.maprecord
for(i in BGCcolors$classification){ zone.maprecord[grep(i,bgc.maprecord)] <- i }
bgc.list <- sort(unique(bgc.maprecord))
zone.list <- sort(unique(zone.maprecord))
# ------------------------------------------
# Define UI
# ------------------------------------------
ui <- fluidPage(
navbarPage(title = paste("BGC projections in climate space"), theme = "bcgov.css",
tabPanel("3D",
fluidRow(
column(2,
helpText("Use mouse to spin and zoom"),
tags$head(tags$script('$(document).on("shiny:connected", function(e) {
Shiny.onInputChange("innerWidth", window.innerWidth);
});
$(window).resize(function(e) {
Shiny.onInputChange("innerWidth", window.innerWidth);
});
')),
checkboxInput("map", label = "Map mode", value = FALSE),
checkboxInput("labels", label = "Show BGC labels", value = TRUE),
selectInput("focal1",
label = "show spatial range of a BGC unit",
choices = as.list(c("none", as.character(BGCs.BC))),
selected = "none"),
selectInput("focal2",
label = "show spatial range of another BGC unit",
choices = as.list(c("none", as.character(BGCs.BC))),
selected = "none"),
checkboxInput("exotic", label = "Include BGC units outside BC", value = FALSE),
conditionalPanel(
condition = "input.exotic == true",
selectInput("focalWNA",
label = "show spatial range of a non-BC BGC unit",
choices = as.list(c("none", as.character(BGCs.WNA))),
selected = "CRFdh_CA"),
),
conditionalPanel(
condition = "input.map == false",
radioButtons("vars", inline = T,
label = "Choose a variable set",
choices = list("Basic" = 1, "CBST" = 2, "CCISS"=3),
selected = 1),
checkboxInput("iso", label = "Equal-scale axes (recommended for PCs)", value = TRUE),
checkboxInput("biplot", label = "Show variable correlations", value = FALSE),
conditionalPanel(
condition = "input.vars == 1",
selectInput("var1.1",
label = "Choose the primary variable",
choices = as.list(c("PC1", "PC2", "PC3", vars.basic)),
selected = "PC1"),
selectInput("var2.1",
label = "Choose the secondary variable",
choices = as.list(c("PC1", "PC2", "PC3", vars.basic)),
selected = "PC2"),
selectInput("var3.1",
label = "Choose the tertiary variable",
choices = as.list(c("PC1", "PC2", "PC3", vars.basic)),
selected = "PC3"),
),
conditionalPanel(
condition = "input.vars == 2",
selectInput("var1.2",
label = "Choose the primary variable",
choices = as.list(c("PC1", "PC2", "PC3", vars.cbst)),
selected = "PC1"),
selectInput("var2.2",
label = "Choose the secondary variable",
choices = as.list(c("PC1", "PC2", "PC3", vars.cbst)),
selected = "PC2"),
selectInput("var3.2",
label = "Choose the tertiary variable",
choices = as.list(c("PC1", "PC2", "PC3", vars.cbst)),
selected = "PC3"),
),
checkboxInput("recent", label = "Show shift to 2001-2019 climate", value = FALSE),
checkboxInput("future", label = "Show shifts to future climates", value = FALSE),
conditionalPanel(
condition = "input.future == true",
selectInput("focal",
label = "Choose a focal BGC unit",
choices = as.list(c(as.character(BGCs.BC))),
selected = "CDFmm"),
radioButtons("proj.year", inline = T,
label = "Choose a future period",
choices = list("2011-2040" = 1, "2041-2070" = 2, "2071-2100" = 3),
selected = 1),
radioButtons("rcp", inline = T,
label = "Choose an emissions scenario",
choices = list("RCP4.5" = 1, "RCP8.5" = 2),
selected = 1)
),
),
),
column(10,
rglwidgetOutput(outputId = "plot", width="86vw", height="86vh")
# plotOutput(outputId = "plot", height="86vh")
),
column(width = 12,
style = "background-color:#003366; border-top:2px solid #fcba19;",
tags$footer(class="footer",
tags$div(class="container", style="display:flex; justify-content:center; flex-direction:column; text-align:center; height:46px;",
tags$ul(style="display:flex; flex-direction:row; flex-wrap:wrap; margin:0; list-style:none; align-items:center; height:100%;",
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home", "Home", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/disclaimer", "Disclaimer", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/privacy", "Privacy", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/accessibility", "Accessibility", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/copyright", "Copyright", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/StaticWebResources/static/gov3/html/contact-us.html", "Contact", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;"))
)
)
)
)
)
),
tabPanel("Find-a-BEC",
sidebarLayout(
sidebarPanel(
helpText("Choose a BGC zone or subzone-variant to show it on the map"),
tags$head(tags$script('$(document).on("shiny:connected", function(e) {
Shiny.onInputChange("innerWidth", window.innerWidth);
});
$(window).resize(function(e) {
Shiny.onInputChange("innerWidth", window.innerWidth);
});
')),
selectInput("showbgc",
label = "Choose a BGC subzone-variant",
choices = as.list(c("none", bgc.list)),
selected = "none"),
selectInput("showzone",
label = "Choose a BGC zone",
choices = as.list(c("none", zone.list)),
selected = "none"),
),
mainPanel(
leafletOutput(outputId = "becmap", height="86vh")
)
),
column(width = 12,
style = "background-color:#003366; border-top:2px solid #fcba19;",
tags$footer(class="footer",
tags$div(class="container", style="display:flex; justify-content:center; flex-direction:column; text-align:center; height:46px;",
tags$ul(style="display:flex; flex-direction:row; flex-wrap:wrap; margin:0; list-style:none; align-items:center; height:100%;",
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home", "Home", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/disclaimer", "Disclaimer", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/privacy", "Privacy", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/accessibility", "Accessibility", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/copyright", "Copyright", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/StaticWebResources/static/gov3/html/contact-us.html", "Contact", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;"))
)
)
)
)
),
tabPanel("About",
includeMarkdown("about.Rmd"),
column(width = 12,
style = "background-color:#003366; border-top:2px solid #fcba19;",
tags$footer(class="footer",
tags$div(class="container", style="display:flex; justify-content:center; flex-direction:column; text-align:center; height:46px;",
tags$ul(style="display:flex; flex-direction:row; flex-wrap:wrap; margin:0; list-style:none; align-items:center; height:100%;",
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home", "Home", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/disclaimer", "Disclaimer", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/privacy", "Privacy", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/accessibility", "Accessibility", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/gov/content/home/copyright", "Copyright", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;")),
tags$li(a(href="https://www2.gov.bc.ca/StaticWebResources/static/gov3/html/contact-us.html", "Contact", style="font-size:1em; font-weight:normal; color:white; padding-left:5px; padding-right:5px; border-right:1px solid #4b5e7e;"))
)
)
)
)
)
)
)
# ------------------------------------------
# Define server logic
# ------------------------------------------
server <- function(input, output) {
output$plot <- renderRglwidget({
variables <- c("PC1", "PC2", "PC3", get(paste("vars", varsets[as.numeric(input$vars)], sep=".")))
variable.types <- rep(NA, length(variables))
variable.types[grep("PPT|DD|PAS|NFFD|Eref|FFP|CMD|MAP|MSP|AHM|SHM|Rad|MAR", variables)] <- "ratio"
variable.types[grep("Tmax|Tmin|Tave|MAT|MWMT|MCMT|TD|EMT|EXT|bFFP|eFFP|PC", variables)] <- "interval"
variable.types[grep("RH", variables)] <- "pct"
# reorder variables
Clim.BGCs.BC <- Clim.BGCs.BC.all[,which(names(Clim.BGCs.BC.all)%in%variables)]
Clim.BGCs.WNA <- Clim.BGCs.WNA.all[,which(names(Clim.BGCs.WNA.all)%in%variables)]
Clim.BGCs.BC.2004 <- Clim.BGCs.BC.2004.all[,which(names(Clim.BGCs.BC.2004.all)%in%variables)]
Clim.sample.BC <- Clim.sample.BC.all[,which(names(Clim.sample.BC.all)%in%variables)]
Clim.sample.WNA <- Clim.sample.WNA.all[,which(names(Clim.sample.WNA.all)%in%variables)]
Clim.BGCs.BC.future <- Clim.BGCs.BC.future.all[,which(names(Clim.BGCs.BC.future.all)%in%variables)]
# PC Scores with log transformation
logT.clim <- function(x){
zerolim <- grep("MAP|PPT|PAS|DD|CMD|NFFD|FFP|MSP|Eref",names(x))
for(i in zerolim){x[which(x[,i]<1),i] <- 1} #set zero values to one, to facilitate log-transformation
x[,zerolim] <- log(x[,zerolim]) #log-transform the zero-limited variables
return(x)
}
pca.BGCs <- prcomp(logT.clim(Clim.BGCs.BC), scale=T)
# Cor <- cor(Clim.BGCs.BC,predict(pca.BGCs, logT.clim(Clim.BGCs.BC)))
Clim.BGCs.BC <- cbind(predict(pca.BGCs, logT.clim(Clim.BGCs.BC))[,1:3], Clim.BGCs.BC)
Clim.BGCs.WNA <- cbind(predict(pca.BGCs, logT.clim(Clim.BGCs.WNA))[,1:3],Clim.BGCs.WNA)
Clim.BGCs.BC.2004 <- cbind(predict(pca.BGCs, logT.clim(Clim.BGCs.BC.2004))[,1:3],Clim.BGCs.BC.2004)
Clim.sample.BC <- cbind(predict(pca.BGCs, logT.clim(Clim.sample.BC))[,1:3],Clim.sample.BC)
Clim.sample.WNA <- cbind(predict(pca.BGCs, logT.clim(Clim.sample.WNA))[,1:3],Clim.sample.WNA)
Clim.BGCs.BC.future <- cbind(predict(pca.BGCs, logT.clim(Clim.BGCs.BC.future))[,1:3],Clim.BGCs.BC.future)
if(input$map == T){
cols <- as.character(ColScheme.zone[match(zones.BC,zones)])
cols.WNA <- as.character(ColScheme.zone[match(zones.WNA,zones)])
x <- Geog.BGCs.BC[, 1]
y <- Geog.BGCs.BC[, 2]
z <- Geog.BGCs.BC[, 3]
if(input$focal1 != "none"){
x1 <- Geog.sample.BC[which(BGCs.sample.BC==input$focal1), 1]
y1 <- Geog.sample.BC[which(BGCs.sample.BC==input$focal1), 2]
z1 <- Geog.sample.BC[which(BGCs.sample.BC==input$focal1), 3]
}
if(input$focal2 != "none"){
x2 <- Geog.sample.BC[which(BGCs.sample.BC==input$focal2), 1]
y2 <- Geog.sample.BC[which(BGCs.sample.BC==input$focal2), 2]
z2 <- Geog.sample.BC[which(BGCs.sample.BC==input$focal2), 3]
}
if(input$exotic == TRUE){
if(input$focalWNA != "none"){
x3 <- Geog.sample.WNA[which(BGCs.sample.WNA==input$focalWNA), 1]
y3 <- Geog.sample.WNA[which(BGCs.sample.WNA==input$focalWNA), 2]
z3 <- Geog.sample.WNA[which(BGCs.sample.WNA==input$focalWNA), 3]
}
}
#core plot with BGC centroids
plot3d(x,y,z, xlab="Longitude", ylab="Latitude", zlab="Elevation",
type="s",
col = cols,
alpha = 0.5,
size=.5)
#BGC labels (bug in package means you need to overwrite a few times to get some to show)
if(input$labels == T){
text3d(x,y,z, BGCs.BC, adj=-0.2, font=2, cex=0.6)
text3d(x[1:30],y[1:30],z[1:30], BGCs.BC[1:30], adj=-0.2, font=2, cex=0.6)
text3d(x[31:60],y[31:60],z[31:60], BGCs.BC[31:60], adj=-0.2, font=2, cex=0.6)
text3d(x[61:90],y[61:90],z[61:90], BGCs.BC[61:90], adj=-0.2, font=2, cex=0.6)
# for(i in 0:5) text3d(x[i*100+1:99],y[i*100+1:99],z[i*100+1:99], BGCs.BC[i*100+1:99], adj=-0.2, font=2, cex=0.6)
# for(i in 1:length(BGCs.BC)) text3d(x[i],y[i],z[i], BGCs.BC[i], adj=-0.2, font=2, cex=0.6)
}
if(input$exotic == T){
x.WNA <- Geog.BGCs.WNA[, 1]
y.WNA <- Geog.BGCs.WNA[, 2]
z.WNA <- Geog.BGCs.WNA[, 3]
plot3d(x.WNA,y.WNA,z.WNA, type="s",col = cols.WNA,alpha = 0.5,size=0.25, add=T)
if(input$labels == T){
text3d(x.WNA,y.WNA,z.WNA, BGCs.WNA, adj=-0.2, font=2, cex=0.6, color="blue")
text3d(x.WNA[1:30],y.WNA[1:30],z.WNA[1:30], BGCs.WNA[1:30], adj=-0.2, font=2, cex=0.6, color="blue")
text3d(x.WNA[31:60],y.WNA[31:60],z.WNA[31:60], BGCs.WNA[31:60], adj=-0.2, font=2, cex=0.6, color="blue")
}
}
#
if(input$focal1 != "none"){
plot3d(x1,y1,z1, col=cols[which(BGCs.BC==input$focal1)], type="s",size=0.2, alpha=0.4, add=T)
}
if(input$focal2 != "none"){
plot3d(x2,y2,z2, col=cols[which(BGCs.BC==input$focal2)], type="s",size=0.2, alpha=0.4, add=T)
}
if(input$exotic == T){
if(input$focalWNA != "none"){
plot3d(x3,y3,z3, col=cols.WNA[which(BGCs.WNA==input$focalWNA)], type="s",size=0.2, alpha=0.4, add=T)
}
}
rgl.viewpoint( theta = 0, phi = 0, fov = 60, zoom = 0.65 )
axes3d(tick=F, xlab="Longitude", ylab="Latitude", zlab="Elevation", col="black")
} else {
proj.year <- proj.years[as.numeric(input$proj.year)]
rcp <- rcps[as.numeric(input$rcp)]
var1 <- if(input$vars==1) input$var1.1 else input$var1.2
var2 <- if(input$vars==1) input$var2.1 else input$var2.2
var3 <- if(input$vars==1) input$var3.1 else input$var3.2
variable.type1 <- variable.types[which(variables==var1)]
variable.type2 <- variable.types[which(variables==var2)]
variable.type3 <- variable.types[which(variables==var3)]
x <- Clim.BGCs.BC[, which(variables==var1)]
y <- Clim.BGCs.BC[, which(variables==var2)]
z <- Clim.BGCs.BC[, which(variables==var3)]
Cor <- cor(Clim.BGCs.BC,data.frame(x,y,z))
x.recent <- Clim.BGCs.BC.2004[, which(variables==var1)]
y.recent <- Clim.BGCs.BC.2004[, which(variables==var2)]
z.recent <- Clim.BGCs.BC.2004[, which(variables==var3)]
bgc.focal <- input$focal
x.future <- Clim.BGCs.BC.future[which(BGCs.future==bgc.focal & scenario$rcp==rcp & scenario$proj.year==proj.year), which(variables==var1)]
y.future <- Clim.BGCs.BC.future[which(BGCs.future==bgc.focal & scenario$rcp==rcp & scenario$proj.year==proj.year), which(variables==var2)]
z.future <- Clim.BGCs.BC.future[which(BGCs.future==bgc.focal & scenario$rcp==rcp & scenario$proj.year==proj.year), which(variables==var3)]
if(input$focal1 != "none"){
x1 <- Clim.sample.BC[which(BGCs.sample.BC==input$focal1), which(variables==var1)]
y1 <- Clim.sample.BC[which(BGCs.sample.BC==input$focal1), which(variables==var2)]
z1 <- Clim.sample.BC[which(BGCs.sample.BC==input$focal1), which(variables==var3)]
}
if(input$focal2 != "none"){
x2 <- Clim.sample.BC[which(BGCs.sample.BC==input$focal2), which(variables==var1)]
y2 <- Clim.sample.BC[which(BGCs.sample.BC==input$focal2), which(variables==var2)]
z2 <- Clim.sample.BC[which(BGCs.sample.BC==input$focal2), which(variables==var3)]
}
if(input$exotic == TRUE){
if(input$focalWNA != "none"){
x3 <- Clim.sample.WNA[which(BGCs.sample.WNA==input$focalWNA), which(variables==var1)]
y3 <- Clim.sample.WNA[which(BGCs.sample.WNA==input$focalWNA), which(variables==var2)]
z3 <- Clim.sample.WNA[which(BGCs.sample.WNA==input$focalWNA), which(variables==var3)]
}
}
cols <- as.character(ColScheme.zone[match(zones.BC,zones)])
cols.WNA <- as.character(ColScheme.zone[match(zones.WNA,zones)])
#core plot with BGC centroids
plot3d(x,y,z, xlab=var1, ylab=var2, zlab=var3,
type="s",
col = cols,
alpha = 0.5,
size=.5)
#BGC labels (bug in package means you need to overwrite a few times to get some to show)
if(input$labels == T){
text3d(x,y,z, BGCs.BC, adj=-0.2, font=2, cex=0.6)
text3d(x[1:30],y[1:30],z[1:30], BGCs.BC[1:30], adj=-0.2, font=2, cex=0.6)
text3d(x[31:60],y[31:60],z[31:60], BGCs.BC[31:60], adj=-0.2, font=2, cex=0.6)
text3d(x[61:90],y[61:90],z[61:90], BGCs.BC[61:90], adj=-0.2, font=2, cex=0.6)
# for(i in 0:5) text3d(x[i*100+1:99],y[i*100+1:99],z[i*100+1:99], BGCs.BC[i*100+1:99], adj=-0.2, font=2, cex=0.6)
# for(i in 1:length(BGCs.BC)) text3d(x[i],y[i],z[i], BGCs.BC[i], adj=-0.2, font=2, cex=0.6)
}
if(input$exotic == T){
x.WNA <- Clim.BGCs.WNA[, which(variables==var1)]
y.WNA <- Clim.BGCs.WNA[, which(variables==var2)]
z.WNA <- Clim.BGCs.WNA[, which(variables==var3)]
plot3d(x.WNA,y.WNA,z.WNA, type="s",col = cols.WNA,alpha = 0.5,size=0.25, add=T)
if(input$labels == T){
text3d(x.WNA,y.WNA,z.WNA, BGCs.WNA, adj=-0.2, font=2, cex=0.6, color="blue")
text3d(x.WNA[1:30],y.WNA[1:30],z.WNA[1:30], BGCs.WNA[1:30], adj=-0.2, font=2, cex=0.6, color="blue")
text3d(x.WNA[31:60],y.WNA[31:60],z.WNA[31:60], BGCs.WNA[31:60], adj=-0.2, font=2, cex=0.6, color="blue")
}
}
#add in Biplot arrows
if(input$biplot == T){
EF <- 3 #arrow length modifier
rgl.lines(t(cbind(rep(mean(x), dim(Cor)[1]),mean(x)+Cor[,1]*EF*sd(x))),
t(cbind(rep(mean(y), dim(Cor)[1]),mean(y)+Cor[,2]*EF*sd(y))),
t(cbind(rep(mean(z), dim(Cor)[1]),mean(z)+Cor[,3]*EF*sd(z))),
color="red")
text3d(mean(x)+1.1*(Cor[,1]*EF*sd(x)),
mean(y)+1.1*(Cor[,2]*EF*sd(y)),
mean(z)+1.1*(Cor[,3]*EF*sd(z)),
rownames(Cor), col="red", xpd=T, cex=0.9, font=2)
}
#
if(input$focal1 != "none"){
plot3d(x1,y1,z1, col=cols[which(BGCs.BC==input$focal1)], type="s",size=0.2, alpha=0.4, add=T)
}
if(input$focal2 != "none"){
plot3d(x2,y2,z2, col=cols[which(BGCs.BC==input$focal2)], type="s",size=0.2, alpha=0.4, add=T)
}
if(input$exotic == T){
if(input$focalWNA != "none"){
plot3d(x3,y3,z3, col=cols.WNA[which(BGCs.WNA==input$focalWNA)], type="s",size=0.2, alpha=0.4, add=T)
}
}
if(input$iso==T) aspect3d("iso")
if(input$recent==T) rgl.lines(t(cbind(x,x.recent)), t(cbind(y,y.recent)), t(cbind(z,z.recent)), color="grey")
if(input$future==T){
rgl.lines(t(cbind(rep(x[which(BGCs.BC==input$focal)], length(x.future)),x.future)), t(cbind(rep(y[which(BGCs.BC==input$focal)], length(y.future)),y.future)), t(cbind(rep(z[which(BGCs.BC==input$focal)], length(z.future)),z.future)), color="black")
}
# rgl.viewpoint( theta = 0, phi = 0, fov = 60, zoom = 0.65 )
axes3d(tick=F, xlab=var1, ylab=var2, zlab=var3, col="black")
}
rglwidget(reuse=T)
},
# height=reactive(ifelse(!is.null(input$innerWidth),input$innerWidth*0.4,0))
)
#-------------------------
# Find-a-BEC
#-------------------------
# showbgc <- "BGxh1"
# showzone <- "BG"
output$becmap <- renderLeaflet({
showbgc <- input$showbgc
showzone <- input$showzone
leaflet() %>%
addTiles() %>%
addProviderTiles("Esri.WorldImagery", group = "Satellite view") %>%
addProviderTiles("Esri.WorldTerrain", group = "Terrain only") %>%
addProviderTiles("Esri.WorldTopoMap", group = "Base map") %>%
fitBounds(lng1 = extent(bgc.simple)[1], lat1 = extent(bgc.simple)[3], lng2 = extent(bgc.simple)[2], lat2 = extent(bgc.simple)[4]) %>%
addLayersControl(
baseGroups = c("Base map", "Terrain only", "Satellite view"),
options = layersControlOptions(collapsed = FALSE),
) %>%
addPolygons(data=bgc.simple[zone.maprecord == showzone,], fillColor = "red", color="red", smoothFactor = 0.2, fillOpacity = 0.4, weight=2, opacity=1)%>%
addPolygons(data=bgc.simple[bgc.maprecord == showbgc,], fillColor = "black", color="black", smoothFactor = 0.2, fillOpacity = 0.4, weight=2, opacity=1)
},
)
}
# Run the app ----
shinyApp(ui = ui, server = server)
# vars <- get(paste("vars", varsets[2], sep="."))
# variables <- c("PC1", "PC2", "PC3", vars)
# proj.year <- 2055
# rcp <- "rcp45"
# gcm <- "CESM1-CAM5"
# var1 <- variables[1]
# var2 <- variables[2]
# var3 <- variables[3]
# x <- Clim.BGCs.BC[, which(variables==var1)]
# y <- Clim.BGCs.BC[, which(variables==var2)]
# z <- Clim.BGCs.BC[, which(variables==var3)]
# BGCs <- as.character(BGCs.BC)
# cols <- as.character(ColScheme.zone[match(zones.BC,zones)])
# bgc.focal <- "BGxh1"